Also correcting some documentation strings.

Global file mode override now works properly with
the file mode stored in the tree node.

Replace with the contents of 
git_index_read_tree_with_stats() and improve
documentation comments.

New variant of git_index_read_tree that fills in
the 'total' field of a git_indexer_stats struct
as it's walking the tree.

Renamed git_checkout_index to what it really was,
and removed duplicate code from clone.c. Added
git_checkout_ref, which updates HEAD and hands off
to git_checkout_head.

Added tests for the options the caller can pass to
git_checkout_*.

Now creating intermediate directories where the
submodule is deep, like "src/deps/foosubmodule".

odb: add some documentation to the foreach() test

Add a struct for network callbacks

Yes, we can get the repository from the owner of the object, but having
it marked explicitly makes the API more consistent.

Add support for push-urls

* Removed the #define for defaults
* Promoted progress structure to top-level API call
  argument